Baby endangered California salmon use different rivers than expected, research shows

Biologists assumed baby winter-run Chinook salmon hung out in the Sacramento River where they hatched until they grew large enough to make the trip downstream to the Pacific Ocean.

A recently released scientific study challenges that assumption – and may have implications in how fisheries agencies manage Sacramento Valley waterways to protect the critically endangered fish.

In a paper published online last week in the journal Biological Conservation, a team of California researchers revealed a surprising finding: Juvenile winter-run Chinook aren’t just using the Sacramento River as rearing habitat; after hatching, they also venture in large numbers into the river’s tributaries, including creeks that feed into it below Redding, as well the Feather and the American rivers.

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A biologist measures a baby winter-run chinook salmon caught in a research trap in the Sacramento River near Knights Landing in this 2005 file photo.

Randy Pench Sacramento Bee Staff Photo

Winter-run Chinook are a distinct species of salmon that return each year to spawn and die in the Sacramento River near Redding. As recently as the 1960s, tens of thousands of adult fish used to make the one-way journey.

Now, as little as a few dozen come back. The population’s steep decline has forced federal water managers to cut back water deliveries from Shasta Dam to farms and cities in some years to preserve cold water the fish need to spawn. Commercial salmon-fishing seasons also have been restricted. Researchers say their findings may eventually lead to greater protections for waterways that hadn’t been considered vital to the survival of the species.

The findings came about after researchers collected tiny ear bones called otoliths from adult fish that had died after spawning. These bones function much like a tree’s rings – distinct layers form around the edges over time as the fish grows.

Scientists typically use otoliths to determine an age of a fish. These researchers used otoliths for a more novel purpose.

As they grow, otoliths absorb isotopes found in the water. The researchers used specialized equipment to take readings of the isotopes in the tiny layers of bone that formed when the fish were young.

Using isotopic readings to determine where fish grew up wouldn’t work in many waterways around the world, but the unique type of rocks – and their distinct isotopic signatures – lining Sacramento Valley rivers and streams gave researchers a precise picture of where the young fish came from, said Anna Sturrock, a UC Davis researcher whose Twitter handle is @otolithgirl.

“You guys are very lucky in California because ... you have all these different rock types – old and new, volcanic, granite – and you end up with this nice amount of variation among rivers that we can use with high certainty to place a fish,” she said.

Chinook live about two years in the Pacific Ocean before adult fish head back up river to spawn and die. Before making the journey to salt water, the juveniles will spend several months in fresh water, growing large enough to make the trip to the sea. Previously, biologists assumed these young fish hatched in the Sacramento River stay there before heading to the Pacific.

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Sturrock’s team was surprised to discover that the isotope data found in ear bone samples taken from adult fish in 2007 through 2009 revealed that up to 65 percent of the fish had traveled off the main Sacramento River channel as youngsters.

The study’s lead author, Corey Phillis of the Metropolitan Water District of Southern California, recalls thinking at first the readings were wrong.

“But then we started presenting this work at conferences, and we keep having (researchers) come up to us and saying, ‘Oh yeah, we would catch (young) fish that are far too large at that time of year to be anything other than winter-run,’” he said.

The findings come at a critical time for the winter-run Chinook. Cut off by dams from the spring-fed, cold-water tributaries in which the species used to spawn, the fish now lay their eggs in the heat of the summer in a short stretch of the Sacramento River below Shasta Dam.

The plight of the winter-run reached crisis levels during California’s historic five-year drought. Warm water below the dam those years was baking winter-run eggs and baby fish, and researchers were reporting record low numbers of juvenile fish heading down river.

The researchers say they’ll continue the study, sampling the otoliths from the surviving adult fish born during the drought when they come back to the Sacramento River to spawn. The hope is that the research will reveal whether juvenile winter-run use different waterways as rearing habitat during drought years.

The research could have implications for fisheries managers.

The findings show that a large percentage of fish that beat the odds and spawned once lived as juveniles in rivers not designated as critical habitat under federal fisheries management plans, said Rachel Johnson, one of the researchers who works for the National Marine Fisheries Service. Johnson’s agency is charged with protecting winter-run Chinook under the federal Endangered Species Act.

“This does give us some new conservation tools to consider, which we weren’t really thinking about in those geographic regions,” Johnson said.